Package: seam 0.1.0

Marketa Barac Makarova

seam: Sparse Extended Analysis of Modules

Provides tools for comparing groups using sparse principal component analysis (SPCA). Includes functions for identifying and visualizing influential variables, assessing variable selection stability through bootstrapping, and exploring associations with clinical traits. SPCA is implemented using the method described in <doi:10.1198/106186006X113430>.

Authors:Marketa Barac Makarova [aut, cre], Jan Kolacek [ctb]

seam_0.1.0.tar.gz
seam_0.1.0.zip(r-4.7-any)seam_0.1.0.zip(r-4.6-any)
seam_0.1.0.tar.gz(r-4.7-any)seam_0.1.0.tar.gz(r-4.6-any)
seam_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
seam/json (API)

# Install 'seam' in R:
install.packages('seam', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/marketa-makarova/seam/issues

Datasets:
  • seam_demo - Simulated expression and trait data for two groups and two modules

On CRAN:

Conda:

1.70 score 3 scripts 16 exports 31 dependencies

Last updated from:f59c58c4dc. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK135
source / vignettesOK181
linux-releaseOK150
windows-develOK80
windows-releaseOK101
wasm-releaseOK120

Exports:compute_activitycompute_module_trait_correlationscompute_variable_trait_correlationsinsight_correlations_lollipopinsight_correlations_reconstructinsight_correlations_sign_changesinsight_weights_lollipopplot_activity_barplot_activity_bubbleplot_explained_varianceplot_lambdasplot_module_heatmapsplot_module_trait_correlationsplot_sparsityspca_all_modulesspca_all_modules_grid

Dependencies:clicpp11dplyrelasticnetfarvergenericsggplot2gluegtableisobandlabelinglarslifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr